Archive 4 checkpoints (1-4)

paper-releases/pbisc-diffusion/updates/20261003T103040Z-crosscohort-k1000-saturation/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/giroux2022/zs_K2000/summary.json

@@ -0,0 +1,531 @@
+{
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+}

paper-releases/pbisc-diffusion/updates/20261003T103040Z-crosscohort-k1000-saturation/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/immicro/locoL_fullsat_s20000_K1000/README.md

@@ -0,0 +1,60 @@
+# score_ft.py output: immicro, 107 scored donors
+
+Arms: locoL_fullsat_s20000_K1000.  Every arm is scored on the same donors against the same observed reference.
+
+## Inputs and fixed contracts
+- Observed reference: `/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/scoring_cache/immicro/reference.npz` (sha c5e2547be3ec), built from datadir:/home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/paired_finetune_intradataset_20260927/data/immicro;
+  observed cells sum exactly to the features pseudobulk of every donor. Observed labels: /home/sj_server_1/PBISC/immun-pbmc-fm/model_8_sparse_data_diffusion/plans/utility_studies_final6k_20260925/immicro/labels/observed_immicro/labels.parquet.
+- Generated cells: `generated_counts` read out once with Poisson(seed 20260916) over the **whole NPZ in row order**
+  (`poisson_readout.poisson_integerise`), then the scored donors' rows. These integer counts are used for labels, embedding,
+  depth and the contrast. Pseudobulk uses the summed `generated_counts` (rates), as `score_generated.py`.
+- Labels: frozen f01common scANVI (`predict_scanvi.py`, CPU, zero query epochs), six-type gate ['T cell', 'B cell', 'Monocyte', 'NK cell', 'DC', 'Other']; query genes =
+  the 1,006-gene annotation list minus genes the dataset's sc assay did not measure in every sample (1004 genes).
+- Scoring genes: 6k panel genes measured by both assays in every sample of the dataset (5508 genes).
+
+## Definitions
+1. **Composition**: fraction of each donor's cells per six-type label (all generated cells; all observed QC cells).
+   `comp_l1` = sum over the six labels of |generated - observed| (immicro_common.l1). `comp_l1_obs_loo_null` = L1 of the
+   donor's observed composition to the mean of the *other scored donors'* observed compositions. `composition_top1` =
+   fraction of donors whose generated composition is closest (L1) to their own observed composition.
+2. **Pseudobulk**: `pb_r` = Pearson r of CPM-log1p(summed generated_counts) vs CPM-log1p(observed pseudobulk) on the scoring
+   genes (evaluate_realbulk.cpm_log1p / paired_r). `pb_top1` = the donor's generated pseudobulk is closest (Pearson) to its own
+   observed pseudobulk among the 107 scored donors (immicro_common.retrieval = evaluate_realbulk.top1 arithmetic).
+3. **Precision / coverage / density** (stage_b_embed.py functions): per-cell CP10K over the scoring genes + log1p; PCA-50
+   (randomized, random_state 20260925) and k = 10 real-real k-NN balls fitted on **R1 of the scored donors only**.
+   Reference rule (independent of fold and arm): per donor, cells in canonical order (library_id+barcode), one
+   permutation from `default_rng([20260925, uint64(sha256(donor)[:8])])`; R1 = first n, R2 = next n,
+   n = min(150, n_cells // 2) (16050 R1 cells here). Generated query: per donor n cells (the donor's R1 size),
+   without replacement, `default_rng([20260926, same key])`. Precision = fraction of generated cells inside any R1 ball
+   (Kynkaanniemi 2019); coverage = fraction of R1 cells whose ball holds a generated cell; density = Naeem 2020.
+   Per-donor precision = that donor's generated cells; per-donor coverage = that donor's R1 cells (the pooled values are
+   their n-weighted means; plain means when every donor has 150 reference cells). R2 (held-out real cells of the same donors) is the
+   perfect-generator control: precision 0.9634, coverage 0.9999.
+   **Depth matched**: stage_b_embed depth matching run pairwise (R1 vs this arm): per donor and within-donor rank of detected
+   genes, both cells are thinned by UMI sampling without replacement to the smaller detected-gene count; PCA kept from
+   un-thinned R1, radii recomputed on thinned R1; fresh rng(20260929) per arm. R2 control: precision
+   0.9635, coverage 0.9997.
+4. **Monocyte %** = 100 x Monocyte fraction (all cells) per donor; **median UMI per cell** = median over cells of the
+   Poisson-read (generated) / observed counts summed over the scoring genes (per donor, and pooled).
+5. **Group contrast** (T, B, Monocyte, NK): not computed (dataset immicro has no group contrast (use --groups-csv / --case-groups)).
+   Genes per type = scoring genes detected (count > 0) in >= 1 % of the scored donors' observed
+   cells of that type. Primary statistic `mean_cp10k`: per-cell CP10K over the scoring genes; per donor the mean over its
+   cells of the type (donors with >= 1 such cell); group mean = mean over the group's donors (donor-balanced);
+   logFC = log2(case mean + 1) - log2(control mean + 1). Secondary `pseudobulk_log1p_cpm`: the SLE benchmark evaluator's
+   statistic (donor x type summed counts, log1p CPM over the scoring genes, mean case - mean control;
+   evaluate_generated_vs_truth.group_log_fold_change). Both are computed on the generated cells (their frozen labels) and on
+   the observed cells; `r_generated` = Pearson r of the two logFC vectors. Broadcast baseline `r_broadcast`: the same
+   observed vector against the logFC of the input bulk (condition NPZ `bulk_counts` of the arm, scoring genes, per-donor
+   CP10K resp. log1p CPM, group means). `partial_r_generated_given_broadcast`: r of the OLS residuals of observed and
+   generated logFC on the bulk logFC (residual_specificity.py).
+6. **Top-50 DEG overlap** (contrast.csv rows `statistic = welch_top50_deg`; summary `deg_top50`): not computed (contrast off).
+
+## Files
+- `per_donor.csv`: one row per arm x donor (all per-donor quantities above).
+- `summary.json`: per arm the donor means / pooled values, provenance (NPZ sha, receipt check, generation metadata,
+  Poisson nnz of the whole NPZ, annotation contract), and the reference block (PCA, R2 control).
+- `contrast.csv`: per arm x cell type x statistic (`mean_cp10k`, `pseudobulk_log1p_cpm`: logFC r; `welch_top50_deg`:
+  top-50 DEG overlap, T / B / Monocyte / NK / DC; columns of the other kind are empty).
+- `arms/<arm>/labels/` (predict_scanvi.py labels + manifest), `arms/<arm>/generated_cells.parquet` (NPZ row, donor, label,
+  UMI on the scoring genes, P/C subsample flag), `arms/<arm>/deg_top50_lists.csv` (observed, generated and broadcast
+  top-50 gene lists, Ensembl ids, rank order).

paper-releases/pbisc-diffusion/updates/20261003T103040Z-crosscohort-k1000-saturation/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/immicro/locoL_fullsat_s20000_K1000/per_donor.csv

@@ -0,0 +1,108 @@
+arm,donor,group,n_generated_cells,n_observed_cells,n_reference_cells,gen_T cell,obs_T cell,gen_B cell,obs_B cell,gen_Monocyte,obs_Monocyte,gen_NK cell,obs_NK cell,gen_DC,obs_DC,gen_Other,obs_Other,comp_l1,comp_l1_obs_loo_null,pb_r,pb_own_rank,pb_top1,precision,coverage,precision_depth_matched,coverage_depth_matched,mono_pct_gen,mono_pct_obs,median_umi_gen,median_umi_obs
+locoL_fullsat_s20000_K1000,HS1,DB1,1500,4384,150,0.6433333333333333,0.6332116788321168,0.10533333333333333,0.05862226277372263,0.066,0.13822992700729927,0.16666666666666666,0.14393248175182483,0.012,0.018476277372262775,0.006666666666666667,0.007527372262773723,0.15913381995133813,0.11035192845413876,0.8966690198083659,3,False,0.78,0.6266666666666667,0.8533333333333334,0.8266666666666667,6.6000000000000005,13.822992700729927,1429.5,1738.0
+locoL_fullsat_s20000_K1000,HS2,DB2,1500,5144,150,0.746,0.661353032659409,0.068,0.05909797822706065,0.05466666666666667,0.1386080870917574,0.11733333333333333,0.11372472783825817,0.007333333333333333,0.02041213063763608,0.006666666666666667,0.006804043545878694,0.194315189217211,0.0929372093835238,0.8923993570914259,12,False,0.7266666666666667,0.54,0.7933333333333333,0.6866666666666666,5.466666666666667,13.860808709175739,1563.0,1429.0
+locoL_fullsat_s20000_K1000,HS3,DB3,1500,4617,150,0.6966666666666667,0.6484730344379467,0.10333333333333333,0.06952566601689408,0.09466666666666666,0.17782109594975093,0.07533333333333334,0.07060862031622266,0.01,0.028589993502274202,0.02,0.004981589776911414,0.20348884557071695,0.053459165242510376,0.8874167714648277,29,False,0.7333333333333333,0.37333333333333335,0.84,0.66,9.466666666666667,17.782109594975093,1690.0,2186.0
+locoL_fullsat_s20000_K1000,HS4,DB4,1500,4167,150,0.7073333333333334,0.54307655387569,0.09933333333333333,0.04535637149028078,0.07666666666666666,0.2371010319174466,0.094,0.14254859611231102,0.009333333333333334,0.02423806095512359,0.013333333333333334,0.007679385649148068,0.44777537796976236,0.2531884543361221,0.8710953251000859,102,False,0.54,0.18666666666666668,0.66,0.54,7.666666666666666,23.71010319174466,1546.0,2111.0
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+locoL_fullsat_s20000_K1000,HS7,DB1,1500,4271,150,0.6833333333333333,0.7035822992273473,0.09,0.03839850152189183,0.086,0.13135097166939827,0.11533333333333333,0.09740107703114025,0.011333333333333334,0.02130648560056193,0.014,0.0079606649496605,0.15114617966128152,0.1475722919611167,0.8945245541349869,6,False,0.7466666666666667,0.7,0.84,0.9333333333333333,8.6,13.135097166939827,1717.5,1748.0
+locoL_fullsat_s20000_K1000,HS8,DB1,1500,3652,150,0.5933333333333334,0.6251369112814896,0.108,0.06489594742606791,0.10666666666666667,0.15553121577217963,0.172,0.11829134720700986,0.008,0.028477546549835708,0.012,0.007667031763417305,0.20229134720700984,0.07029362012561938,0.9010089400405307,3,False,0.7733333333333333,0.6666666666666666,0.8666666666666667,0.9466666666666667,10.666666666666668,15.553121577217963,1551.0,1817.0
+locoL_fullsat_s20000_K1000,HS9,DB3,1500,3942,150,0.724,0.6958396752917301,0.06933333333333333,0.028665651953323185,0.10266666666666667,0.18670725520040587,0.08,0.049974632166412986,0.012,0.03373921867072552,0.012,0.0050735667174023336,0.21155961440892943,0.17742174456702342,0.8936516321681787,12,False,0.76,0.3466666666666667,0.8933333333333333,0.7666666666666667,10.266666666666667,18.670725520040587,1993.0,2389.0
+locoL_fullsat_s20000_K1000,HS10,DB4,1500,4115,150,0.6206666666666667,0.5244228432563791,0.204,0.18347509113001215,0.08266666666666667,0.13001215066828675,0.076,0.13754556500607534,0.009333333333333334,0.021385176184690158,0.007333333333333333,0.0031591737545565005,0.24188578371810454,0.31297998407958516,0.8784169328659995,60,False,0.6533333333333333,0.14,0.7733333333333333,0.6333333333333333,8.266666666666666,13.001215066828674,1423.0,2063.0
+locoL_fullsat_s20000_K1000,HS11,DB6,1500,2886,150,0.6733333333333333,0.6056826056826057,0.10533333333333333,0.061330561330561334,0.10933333333333334,0.24358974358974358,0.094,0.04054054054054054,0.006,0.04573804573804574,0.012,0.0031185031185031187,0.34798891198891196,0.2018289947837638,0.8782379425107587,95,False,0.7866666666666666,0.23333333333333334,0.8,0.5533333333333333,10.933333333333334,24.358974358974358,1617.0,2216.5
+locoL_fullsat_s20000_K1000,HS12,DB2,1500,5035,150,0.7273333333333334,0.6798411122144985,0.088,0.06971201588877855,0.08066666666666666,0.1529294935451837,0.08266666666666667,0.064746772591857,0.007333333333333333,0.025223435948361468,0.014,0.007547169811320755,0.1803058589870904,0.09113833236975562,0.8902843375082071,28,False,0.7533333333333333,0.5333333333333333,0.8266666666666667,0.7133333333333334,8.066666666666666,15.29294935451837,1735.0,1550.0
+locoL_fullsat_s20000_K1000,HS13,DB5,1500,4792,150,0.7026666666666667,0.6156093489148581,0.076,0.056343906510851416,0.11733333333333333,0.2166110183639399,0.07933333333333334,0.08764607679465776,0.009333333333333334,0.02003338898163606,0.015333333333333332,0.0037562604340567614,0.23658096828046743,0.10109004194198506,0.8831651770769454,67,False,0.7066666666666667,0.22666666666666666,0.8,0.6333333333333333,11.733333333333333,21.66110183639399,1845.0,2176.0
+locoL_fullsat_s20000_K1000,HS14,DB3,1500,4235,150,0.5913333333333334,0.6517119244391971,0.10733333333333334,0.06517119244391972,0.12466666666666666,0.20306965761511217,0.144,0.04250295159386069,0.018666666666666668,0.0332939787485242,0.014,0.004250295159386069,0.3068177882723336,0.12046829259489143,0.8984603486840232,26,False,0.7666666666666667,0.43333333333333335,0.8333333333333334,0.7733333333333333,12.466666666666667,20.30696576151122,1732.0,2164.0
+locoL_fullsat_s20000_K1000,HS15,DB4,1500,4592,150,0.5473333333333333,0.46972996515679444,0.10733333333333334,0.04638501742160279,0.172,0.37282229965156793,0.152,0.08776132404181185,0.009333333333333334,0.0195993031358885,0.012,0.0037020905923344947,0.42217653890824625,0.41645998718304533,0.8811013482671409,89,False,0.72,0.16,0.74,0.5133333333333333,17.2,37.282229965156795,1262.5,2302.0
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+locoL_fullsat_s20000_K1000,HS19,DB5,1500,4133,150,0.672,0.5971449310428261,0.15533333333333332,0.1454149528187757,0.078,0.14686668279699977,0.074,0.09145898862811518,0.011333333333333334,0.014275344785869828,0.009333333333333334,0.004839099927413501,0.17853536575530288,0.14309888083913158,0.8799520253748584,66,False,0.66,0.15333333333333332,0.74,0.5866666666666667,7.8,14.686668279699976,1513.5,1955.0
+locoL_fullsat_s20000_K1000,HS20,DB7,1500,1366,150,0.7026666666666667,0.7657393850658858,0.14866666666666667,0.09882869692532943,0.07666666666666666,0.08345534407027819,0.05466666666666667,0.029282576866764276,0.0033333333333333335,0.015373352855051245,0.014,0.007320644216691069,0.16380283064909715,0.3077607388488665,0.8821611353976224,48,False,0.82,0.22666666666666666,0.88,0.7733333333333333,7.666666666666666,8.345534407027818,1988.0,2271.0
+locoL_fullsat_s20000_K1000,HS21,DB1,1500,4748,150,0.5633333333333334,0.5945661331086773,0.12733333333333333,0.06887110362257792,0.12266666666666666,0.1941870261162595,0.15333333333333332,0.11141533277169334,0.009333333333333334,0.02401010951979781,0.024,0.0069502948609941025,0.23485987082280255,0.10176465591941555,0.9012945808620682,4,False,0.72,0.8066666666666666,0.8666666666666667,0.9733333333333334,12.266666666666666,19.41870261162595,1682.0,1849.5
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paper-releases/pbisc-diffusion/updates/20261003T103040Z-crosscohort-k1000-saturation/diffusion/dataset/server_1/model8/plans/paired_crosscohort_20261002/scores/immicro/locoL_fullsat_s20000_K1000/summary.json

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